We present the first pipeline to systematically identify and measure changes in Ψ in alternative splicing events across different genomes without annotation. Our method identified ~15,000 one-to-one orthologous alternative splicing events across human and 4 non-human primates. We show that alternative splicing events are increasing in abundance in every human tissue relative to non-human primates. Additionally, contrary to the tissue-dominated conservation pattern of gene expression, we show that most tissues except for brain, heart, and muscle, have a species-specific splicing pattern. Using these orthologous events, we identified 3,954 significant differential splicing events in 1,807 genes between humans and non-human primates. This thesis represents is part of the ambitious goal towards quantifying all of the changes in genomic complexity that occur between primate species. We provide evidence that these changes could be part of the "missing" genomic basis for the origin of human-specific traits.